I hate the later versions not because of the ravines, the mines and pistons, but:
Villages - Paths are borked. I'm sorry if that wasn't clarified in the previous post, but yeah, the village gravel roads are almost always unaligned, requiring some work in order to make it not look like crud.
Endermen - Because they pick up blocks? Fortunately, the nerf has significantly lowered the amount of blocks they pick up. Basically, in the old versions, given enough time, endermen could totally level a chunk. Now, they can only destroy mud huts and gardens. Wouldn't be a problem, honestly if they dropped the block they were holding, which is something they don't do.
The End - It was honestly lacking, and the Enderdragon just bumped into you as a means of attack. Would be fun if it had more attacks, but right now, it's more or less a battle of attrition. Oh, and endereggs have no use.
More meta stuff:
Block IDs - Only applicable to people who install mods, but the fact that the ID limit increase is already there, but the game thinks it doesn't exist kind of sucks. Personally, I don't hate this much, but yeah, for mod players, this really limits their own choices.
Current snapshot stuff:
SSP+SMP merge - Oh come on, I don't want to play multiplayer while I singleplayer.
Enderchests - Can only contain one inventory per world, which means that in servers, you can only make 1 mega storage (by this, I mean a warehouse hub, much like a bank), and even then, someone with enderstorage could intercept your item trade to someone else. Don't mind this much, personally.